The images from the ocean bed were a cause for celebration for the team of investigators on board the Alucia, off the northern coast of Brazil.

For nearly two years, searchers have been scouring the Atlantic on and off in the hope of finding the Air France Airbus A330-200 that fell out of the sky on its way from Rio to Paris, and there it was. At least part of it – a pair of wheels resting on the seabed nearly 4,000 metres from the surface, two engines and a large part of the fuselage – was still intact.

Then, from the sunless depths, came other images no one had expected. As the Remus robot submarines swept the submerged wreckage, there, clearly visible, were the bodies of some of the 228 passengers who perished when flight AF447 plunged into the sea, several still strapped into their seats.

After the information was relayed back to Paris, it fell to Nathalie Kosciusko-Morizet, minister for ecology and transport, to break the news. "There are bodies still in the part [of the plane] that has been found," she told French radio. "I'm not an expert, but it appears the whole thing didn't explode … there is a part of the cabin, and in that part of the cabin there are bodies" – bodies, she added, "that could be possibly identified". She said France would begin an operation to bring the wreckage and human remains to the surface within the next few weeks as the search to find the plane's flight recorders, the black boxes that may solve the mystery of the crash, continues.

The recovery operation will cost an estimated €5m (£4.4m) and will be financed by the French state, but is expected to cause controversy and arguments between relatives of the victims.

Robert Soulas, vice-president of a support group for the victims' families, said raising the bodies was a thorny question. Among those killed were passengers from France, Britain, Brazil, Italy, Ireland and China. Among several children to die on the flight was the 11-year-old British schoolboy Alexander Bjoroy, who was travelling back to the UK with a chaperone after spending the half term break with his parents in Brazil.

"There's a very traumatic side to this and it causes problems of identification. We don't know what state they are in. And it risks causing a dispute between families who want to leave the bodies at the bottom of the Atlantic and those who want them brought to the surface," Soulas said.

For the families of those who died in the tragedy on 1 June 2009, the discovery of the wreckage marked the first breakthrough in nearly two years and brought a mixture of hope and despair. "We want to know what happened in that plane," said Michel Gaignard, who lost his sister in the accident.

An unnamed lawyer for several of the families said some had still not come to terms with their loss. "There's been no burial, no goodbye … just lots and lots of suffering," he told French radio.

In the days after the crash about 50 bodies and parts of the plane – notably the tailfin – were pulled from the sea by the Brazilian navy. But since then there has been nothing.

It was, as one expert said, "like looking for a needle in a field of haystacks". Three previous search missions had already cost €21.6m and failed to find anything, but with Air France and Airbus, the plane's operator and manufacturer, facing manslaughter charges, there was a legal and financial impetus to continue the search.

The search boat Alucia, operated by a dozen specialists from the Woods Hole Oceanographic Institution in Massachusetts, had left the port of Suape in Brazil on 22 March and arrived two days later in the zone where it hoped to find the aircraft wreckage. Three robot submarines, similar to those used to find the remains of the Titanic in 1985, found traces of the plane on Sunday as they scoured the seabed at a depth of 3,800 and 4,000 metres.

Scanning a circle with a circumference of around 75km from where the plane is thought to have crashed, the robots sent pictures back of wreckage on the seabed a few hundred metres west of the last known position of the plane.

After verifying the photos, investigators aboard the Alucia confirmed it was the missing Airbus A330.

Flight AF447 sent out 24 automatic messages signalling system failures in the moments before it plunged into the sea. The autopilot was also disengaged, but investigators are unsure whether it was turned off automatically or by the pilots.

Preliminary investigations have suggested the plane's speed sensors may have been faulty. Several incidents involving the sensors had been reported to the air authorities before the crash. Other theories include pilot error and unexpected weather conditions.

The debris is concentrated in one zone, suggesting the plane did not explode in flight but hit the water intact. However, investigators say they are continuing to search for the jet's flight recorders, which they say are the only hope of finding out what caused the crash.

The Airbus chief executive, Tom Enders, said: "We strongly hope the discovery of the wreckage will allow us to find the two records, because they are essential to understanding this terrible drama."

The head of France's air accident investigations bureau, Jean-Paul Troadec, said the Alucia did not have the necessary equipment to raise and recover the wreckage, but its crew would continue to gather more detailed images of the remains of the aircraft.

• This article was amended on 5 April 2011. The original standfirst said Flight AF477 went down on its way to Rio. This has been corrected.